Run away, My little Spy (On Hold)
by Jessamine Willow
Summary: Clary had left her father, Valentine. Valentine was the most, well-known person that lived to go against the Clave, the ruling body of the shadowhunters, a league of spies dedicated to hunting the injustice in the shadows. Clary left to keep her loved ones safe from his power. She knew he wanted her, and he was going to have to fight, if he wants to win. Rated T to be safe. AU
1. Chapter 1: Welcome

Chapter 1: Welcome

Clary had gotten the order to go and spread the news of the new initiates coming in later that day. She went around all of the New York institute and handed out the flyer that said she was taking over the new group, and would be her responsibility. Clary was always amazed at how well the institute always looked. So elegant, and shiny, strange for a spy agency. She walked around just admiring the dangly chandeliers and the marble floors, to the old Victorian elevator. For a spy agency, it was quite a conflicting image.

Clary had joined the agency mostly of out desperation. She had to run away. She ran away from her father. Valentine. He was so cruel. He never cared about her wellbeing, he only wanted money and power. Clary's mother, Jocelyn, had left Valentine when she was young and left Clary to defend herself, but Clary has kept close contact to Jocelyn. Jocelyn had said, '_You can't come Clary. You have no idea how much I want to bring you with. But it's not the right time. If Valentine finds you're gone, he'll kill you. Wait until I say.' _Clary waited until she couldn't anymore. Valentine had left New York one weekend, and Clary made her escape. Valentine thinks she's dead, only because of the agency. She has to stay undercover. Clary left out of desperation, because Valentine had gone too far. Valentine had started to kill people to get his company on top, and to keep _others_ quiet. Clary had left and sent a letter to her mother. She told Jocelyn that she had to leave because she was afraid she was next, if she made a wrong move. Jocelyn understood and accepted it. Jocelyn thought it was fine, not great, but doable. Clary thought maybe by joining the agency she would be able to defend herself and hurt Valentine if needed, and it would be a great cover for her, from him.

Clary had gone to her room to dress "properly", according to her head agent, Hodge Starkweather. She went up to her room, and changed into her gear, consisting of lots of leather, especially black leather. She decided since no body was coming for a while that she could sit and draw. Clary loved to draw. She would draw whenever she could, any time of the day, every day. She never got to draw many places of the institute. Like the greenhouse, or the wide-open kitchen, or even the small but cozy living room. She had the first door on the left room, upstairs. She figured the recruits could have the rooms around her, since there's so many of them, why not put them around her so she can bug them. But as much time as she has spent there, she never really took in the beauty of it all.

After Clary had finished her drawing of her room, she decided that she would head off to the training room. She had just walked in when her phone went off.

"Hello?" she asked.

"Clary, your new recruits are here," Hodge said to her with a stern voice. Clary thought Hodge was always a little on edge all the time.

"I'm coming." With that she clicked off her phone and headed down stairs. She walked down stairs to see two boys and one girl. There was a black haired man about 18 years old, with a sporty build and a strong sense, from what she could tell he would be good with a bow, not really needed but nice to be able to uses a bow. Next, there was a girl about Clary's age, long black hair and was wearing heels. Clary thought the girl would be very feisty and has a great arm, good for bats and whips. Last, there was this boy about 17 years old and had golden blonde hair. Golden eyes and looked as if he had a trick up his sleeve, but seems distant. He looks as if he close with them all, so Clary suspects they're all family. '_I hope they can work well under pressure,_' Clary thought.

"Hello, and welcome to the New York Institute. This is the HQ of the Shadowhunter's Spy Agency, in the New York division. We do have other locations listed in the office if you would like transfer. We call ourselves shadowhunters mostly because we hunt in the shadows. We look for justice unidentified, and make sure it is taken. This is Clary, our top instructor. She will be training you for your missions to come." Hodge introduced them to this whole operation and Clary found that they we're slightly ecstatic but at the same time confused.

"Hi, I'm Clary," Clary politely said.

The blonde boy spoke up first, "Hi I'm Jace, and that's Alec and that's his sister, Isabelle." Both Alec and Isabelle said hello and kept quiet.

"Well, can I give you the tour?" Clary asked being as nice as possible.

"That would be lovely," Jace replied with a smirk. Clary thought that Jace was almost flirting with her.

"As Hodge said I am your instructor, so this is where you'll be sleeping. These are your rooms, you all can pick which room you get." Isabelle went straight for the one across from me. Jace went to the one next to Clary and Alec to the one next to Jace. They all settled and never came out again. Clary was a little baffled at the thought of them not doing the tour, but maybe another day. So, Clary went to find Hodge.

Clary left the corridor and headed back downstairs. She thought that if they really wanted a tour they would find her and let her know. But, until then she decided on that she would let Hodge know what she did and headed down to the training room.

Clary walked down to the training room and opened the heavy doors to find Jace hitting a dummy. "Well, it's good to see you found this room," Clary said with a sarcastic tone. Jace stopped what he was doing and looked straight at her almost looked as if he was hurt, but then smirked.

"Well, if I'm going to be better than you I need to get as much as training as I can get," Jace remarked. Clary grabbed a knife and through it. It landed right in the bull's eye on the dummy and had scraped Jace's ear.

"You-"Jace stopped himself and continued, "Nice hit."

Clary smiled, "thanks." She grabbed her weapons and continued what she wanted to do as Jace finished his practice and headed out.

"She's not bad...," Jace said under his breath.


	2. Chapter 2: New Identities

Clary had gotten up pretty early to wake the recruits. "Rise and shine, recruits!" She heard what sounded like two people fall out of bed and one get up and out nicely. She guessed whoever gotten up nicely would be the one to come out first. Of course, it was Jace.

"Morning!" he said as he went around Clary and headed downstairs.

"Breakfast is ready…," Clary began as Jace left and Alec and Isabelle came out of their rooms. All of them were wearing their gear and ready to go.

When Clary had reached the bottom of the steps and entered the kitchen all of them were already eating and chatting. It wasn't until Clary turned behind her to see Hodge was there and they recruits got quiet. "Morning Hodge!" Clary spoke up.

"Good morning," he said quietly. Hodge sat down and began to eat when he noticed the recruits were staring at him.

"Well, you may continue eating, I'm not stopping you." And with that they all continued to eat, in silence.

After breakfast Clary cleaned the plates and gathered her team to lead them to the training room. "This is where you'll be training, with me. Now, you are allowed to come here any time you like but most training is done every day from 7 am till about noon, then you'll be in the class room with Hodge learning about the rules and regulations and what our job is. Alright, everybody pair up." Alec immediately grabbed Jace and Jace shrugged his shoulders at Isabelle.

"Well, Isabelle it looks like you're going to be with me," Isabelle looked around and didn't seem to mind. "That's fine and just call me Izzy." Clary nodded and grabbed throwing knives to begin.

"We're going to start with something easy; throwing knives. When you grab the hilt, grab it, but don't give it a death grip. When you throw, don't fling your wrist and let the dagger fly out of your hand. This shall give you pretty good aim and precision." Jace, Alec and Izzy all threw knives with excellence and it didn't take long for them to learn.

"Good job," was all Clary could say. She felt as if she was teaching them something they already knew.

They continued with the basics of balance, throwing, striking, hitting, blocking, stealth, anything that would give them a good foundation for Jonathan, her brother, would take over. "Well, well, what do we have here, new recruits?" he said with a smirk, wide on his face.

"Everyone, this is my brother Jonathan, he'll eventually train you as well. I'm only for basics and specialized training later on."

Jonathan just looked at them all and nodded, "they will be good when we start missions again." Hodge came in and ordered Jonathan to leave. "Goodbye," he said, and left. Clary still couldn't believe he was her brother. He was stocky and muscle like their father but frail like their mother, Jocelyn. He had snow white hair had a love for stealth and merciless killing, by a few accidents on missions.

When Clary first arrived she found her brother already here. He was abounded years ago, because Valentine wouldn't let Jonathan do his bidding. But, when Clary arrived he seemed to have forgiven their father and moved on, but Clary always thought he was just waiting to strike.

Clary couldn't help but watch her brother walk away so obedient, it didn't seem like him. _'Maybe he is starting to break,'_ she thought. She ridded the thought and continued her teachings, but she couldn't help but notice that Jace was staring at her the whole time.

When they had finished she heard her phone ring. "Hello?"

All she heard was silence and finally he spoke, "Clary? Hey! Um, Rebecca is back in town and I was wondering if you and your family would like to come over and have a huge welcome home party?" And Clary couldn't help but smile about her best friend, Simon. His sister has been going to college away from New York and was coming home, so he wanted to know if she would come over to help him set up the decorations, in her own words. "Yes, Simon I will come over and bring Luke and mom."

'_Luke,'_ she thought, '_I should go see if he's at the shop.' _

"Alright see you later Fray!" he said and he clicked off.

Jace being nosey piped up. "Who was that?" She turned around to face him as Izzy and Alec were cleaning up and putting away the weapons.

"A friend of mine, Simon, his sister is coming back today from being out of state and wants to throw her a party," she said as she gave a smile.

Jace smiled back, "well I guess we'll see you there," and turned away and left.

"Wait…Jace what?!"

Clary realized that they were probably going to come so she decided she had to figure out how to apologize to Simon for the unexpected inconvenience. But, first to see Luke. She went down a couple blocks from her apartment to find a little run down shop full of books and supplies, including a couple weapons here and there. "Luke?" She walked around the store to find him sleeping in the back on a couch. She looked over to see her bag was still here from the last time she spent the night here.

"Huh-what? Clary? Oh, what are you doing here?" She grabbed her bag and shoved him in the stomach with her bag, to wake him up.

"Well, for starters waking you up, second getting my bag, and third Simon is having a party for his sister and he wants us there, all of us." He looked at her and sighed. Clary always thought he looked a little shaggy but strong and caring. He had beady eyes but a softness in the heart. "Fine, I'll go."

She jumped and hugged him, "thank you." He hugged her back and she went started to head home.

She was walking home when she noticed some people heading into a club; she noticed that they looked familiar. She followed them in and tried to blend in with the crowd. She kept her distance and watched them. They approached a man and questioned him, until they stabbed him. Clary almost screamed, but what stopped her, she couldn't believe. The people that were killing the man were her recruits, all three of them. Jace, Alec and Izzy.


	3. Chapter 3: He's Back

Clary didn't know what to think. Her recruits just questioned a man, dragged him to a closet and killed him. _'No one noticed,'_ she thought. Clary ran out of the club and headed to Simon's house. _'They killed a man, cold blooded too. But, they knew how to kill without a sound made, they have training. Why, are they here then?'_ Clary thought. She had one thought after another go around her head, dizzying her by the second. She had a point, she decided she must found out.

Clary arrived at Simon's house, to find that his sister Rebecca answered the door. "Hey, Clary! It's good to see you!" Rebecca hugged Clary and welcomed her in the house.

Clary hugged Rebecca back and walked into the living room to find Simon and his mom laughing. "Hey, Fray. What's up?" Simon asked.

"Well, I need to talk to you about what you called me about." Simon's mom, Elaine, smiled, but Rebecca had a questioning look on her face, but dismissed the thought. Simon, was about six feet tall, brown hair and eyes, and wore big framed glasses. Rebecca was about as tall as Simon and had the same brown eyes, which seemed to shimmer in the sun. Clary doesn't really remember how she met Simon. She just figured he was there one day and has stayed since. Of course, Simon and Luke know of her being a spy, and so does her mom, Jocelyn, they all understood and was fine with her reasoning.

"So, what's up?" Clary panicked. She didn't want to tell Simon, but she had to, and there's the whole dead body thing. Clary knew she couldn't tell anyone about the body, so she swore she wouldn't. "So, I got Luke and mom to come, but I may have a few friends come as well," she said with a smile.

"Clary!" Clary smiled a little less with Simon's retort.

"What, they invited themselves! And, they may not be as bad as you think." Simon gave her a stern look. He didn't really want them there, but he reasoned.

"Fine. Just let me know, who's coming, before you show up, please and thank you." Clary smiled and nodded like a six year old does when they're given a favor to do.

Clary came downstairs and left, so Simon could catch up, for his sister's absence. Clary headed back toward the Institute when she heard her name being called, by a man over at the street corner. "Who's there?" The man walks toward. Clary realizes who it is. Jonathan.

"Clary…what are you doing out here so late?" Clary thought about criticizing him, but he is one not to judge without him judging you more.

"Well, I had to go talk to Simon about the party he's throwing for his sister." Clary decided that she would head back later around when the party started. Jonathan nodded his head and backed off of Clary a little, but not enough to make it feel less awkward for her.

"Very well. You shouldn't be out here so late, but for that reason I will let this slide. Hodge wants you back now, by the way." Clary watched as her brother disappeared into the fog rolling in.

"Okay."

Clary had entered the Institute to find all three of her "friends" talking to Hodge. "Clary! Where have you been?"

Clary came in and took off her bag. "Um, I went to see Simon. He's arranging a party for his sister, now how many times do I have to say that?!"

Hodge shook his head, "I don't need you running around, when Valentine is out there, ready to kill you any second." Clary snapped inside.

"Really Hodge? You care about me? That's nice to know." Hodge shook his head again, and everyone else stepped back away from the boiling pot called Clary.

"Clary, I'm sorry, that none of us were there to protect you. It would've been best if your mother took you with her, but she didn't, and I am truly sorry, but he's made an appearance again." Clary stopped lashing out and looked at her recruits, then back at Hodge, questioning whether he was telling the truth, and if they should hear this.

"Hodge, what do you mean?"

Hodge gave her a sorrow filled smile, "he made a kill, with his signature." Clary had started to break down, as Jace and his siblings had just stood there speechless.

Clary had gone from a sob to a full on cry. Valentine was a rogue spy. He did want he wanted and didn't care about your opinion on it. His "operations" considered of trying to "fix" the Clave, according to him. Valentine once had tried to take down the Clave but didn't succeed, but he did create the Circle. The Circle was a group of spies, including Hodge, Jocelyn and Luke, that were trying to change the Clave but that's not easily done. Since the fall, he has been trying to do it all on his own, and since Clary didn't go with her mother, she was left to do the dirty work.

'_No, no this can't be happening. I thought…I thought he stopped. I should've known.'_ Clary thought. Hodge was trying to comfort her when Jace stepped up.

"Clary. Clary! You'll be fine. I've been spy for over a third of my life and I will do anything to protect you. You understand?" Clary stopped crying. She blinked a couple of times and it hit her. _'He's been doing this for over a third, he has had training, liars. How can he protect me, when I can't even trust him?'_ she thought again as Jace had started to pull her up.

"Okay, Jace." Jace picked her up and brought her over to a chair. Jace could see the horror and confusion in her face, he never felt so bad for a girl he barely knew, but maybe it wasn't sympathy, but empathy. Jace's face changed. He went for someone caring about this girl, to someone full of rage.

"Jace where are you going?" Alec said as he caught Jace trying to leave the Institute.

"To find Valentine."


	4. Chapter 4: The New Circle

_**A/n: SO, since I just realized this, and not many people will read my profile. I do not own The Mortal Instruments. Disclaimer done. Enjoy!**_

"Do you really think you can defeat him?" Alec had said has he caught up to Jace.

"It's worth a shot." Alec knew where this was going.

"Jace, don't. Don't do this. I don't want this to be like last time. Maybe we should tell her."

Jace spun around to face Alec was furious, "Alec! It won't be like last time, I promise. I would rather not tell Clary but, you might be right." Alec nodded his head as Jace walked out into the night to find Valentine.

"Clary?" Clary heard whispers of her name. She opened her eyes to see Simon, Izzy and Alec staring at her.

"Clary?" She finally realized that Simon was calling her.

"Simon?" Everyone sighed in relief, she was alive. Clary sat up, "what happened?" Simon looked at Izzy and Alec. He got up and let Alec sit down.

"Simon, knows more than he should, for not being a spy but this concerns a lot about you, by the way you were out for two days. Stress, is a deadly poison. Anyway, Jace left to find Valentine. And, were not exactly what we say we are." Clary blinks her eyes and looks at Simon, he seems tense, like he wouldn't know Clary's reaction.

"I know." They all look at her in surprise.

"You do?" Izzy asked.

"Yeah," Clary said shyly.

"When I left Simon's house to come back here, I saw you three go into that club, and I followed you. When I went in, I saw you three talking to some guy, and then you killed him. I ran out as soon as I could, so you wouldn't recognize me and came back here." They all had their mouths open, even Simon.

"You knew?" Isabelle questioned.

"Why didn't you say something? This could've been better!" Clary questioned Izzy in her head. '_Izzy what are you talking about?'_ It seems Alec heard her.

"Izzy, isn't exactly herself. A while ago, we were hunting-," Alec stopped and thought about what to say,

"Let me start from the beginning." Clary nodded and got up out of the bed.

They walked to the library. As Clary showed Alec the way, he began, "My family comes from a line rogue spies, we do deeds no one else would. '_Justice is in our hands,' _as the motto goes. We were called to find a girl with red hair in New York, now we know it's you. We were told she was of importance, since '_her father was Valentine._' We were told Valentine was the leader of the Circle, a group that went against the Clave to try and bring a new order. We were told to find her and bring her on our side so we could bring down Valentine. That was our job, and now I'm not sure if it was successful.

"Izzy is upset because on trying to find you, Jace got in a few problems with some people that worked for Valentine and our little brother Max got in the way and was killed. Iz, doesn't want Jace to end up like Max. We killed that guy because he worked for Valentine. Clary, we're not normal spies. We're rogues." Clary stopped in front of the weapons room.

"Why are we here?" Clary turned around to Alec.

"Look, I don't care what you were, it depends on now what you do, if I like you or not. At some point we all go rogue, but at some point we all go back. I've already done that, now you all get too. Join me, join us. And we'll together bring down my father. He never was my father anyway." Clary walked away from Alec and went to find Hodge. Alec stood there thinking, contemplating her words, '_at some point we all go back, I've already done that.'_

"She went rogue to Valentine, but reclaimed herself here. She has come back."

Jace looked around for something that might lead to Valentine. Anything a normal spy wouldn't see. "Jonathan?" he whispered. Jonathan was there talking to some man.

"We're near Simon's house. What is he doing here?" The man left and Jonathan was alone. Jace jumped from the tree he was in.

"Jonathan!" Jonathan turned his head and looked at Jace.

"Jace, it's nice to see you, but why are you here?" Jace smirked.

"You must know who I am? 'Jace the best rogue out there!' You must've see the headlines." Jonathan smirked.

"Well, then you must know I'm not one of popularity, I like the shadows." Jonathan had begun to leave when Jace stuck a knife to his throat.

"Look, I now you're working for Valentine, I know everything you said to Clary was a lie, she never really did anything." Jace left, he knew Jonathan would send his message along. Jace walks in and finds Clary carrying weapons from one room to another.

"What are you doing?"Jace asks. Clary looks at him.

"Ask Alec." Clary points to where the library is. Jace follows the finger and finds Izzy, Alec and Simon all chatting with Hodge.

"Jace! Welcome my boy, you're just in time," Hodge says as Jace feels a hand on his head.

"Hello Jace." Izzy turns around and runs up to a woman.

Hodge sets his stuff down and follow her. "Hello, Maryse."

Maryse looks around. "Hello, it's good to be back."

Alec and Izzy catch up with Maryse while Hodge talks to Clary about her plan. "So, do you know her plan?" Jace asked.

Simon looks up, "well, I guess you don't really know her yet if you can't figure it out." Jace looks down shadily upon Simon, "I know her plan; I just don't like it. I was hoping she had a different one I didn't know about."

Simon nods his head, "me too."

Everyone gathers together and Clary begins, "Well, yes Valentine is my father, but no I don't consider him my own. Jonathan is my brother, but again, never as my own. What I'm saying is, I never really trusted either of them. I never really did anything for Valentine and found it hard to believe that Valentine would throw away his son, "who had no potential". All I'm saying is, I want to know everything you got on him and my brother. I have feeling they are working together, and I'm willing to bring them down, but I need some help. So, will you join the Shadowhunters, and reclaim your name?"

Izzy and Alec were the first to speak, then Hodge then Maryse. "Yes."

Clary looked over to see her mother and Luke standing there, hand in hand, and saying yes.

"Jace?" Clary heard Izzy ask. He was the only who hadn't said anything.

"Jace!" Alec said.

"I don't know…" is what Jace said.


	5. Chapter 5: He knows

_**A/n: Hey! I'm so sorry it took me a while to write this chapter. School started so I don't have as much time, but I will finish this story. I love it too much to stop. :P so, enjoy and please review and I hope you love it just as much as me. :) **_

"What do you mean, 'you don't know?'" Clary asked. Jace looked around and knew he had at least 10 pairs of eyes on him.

Jace knew he had to pick his words carefully. _'If I say that I up for it, then that means I'm okay with her plan, when I'm not. But, if I say I'm not with it, they'll think I'm a traitor or at least Clary, Izzy and Alec will,'_ Jace thought.

"Fine. I'll follow your plan Clary, but just know I don't like it. I will claim my name as a Shadowhunter, and I will join your institute Hodge, but, what exactly do you plan to do Clary, just hit Valentine and Jonathan until their knocked out?"

Clary shook her head. "To be honest, I never thought I would make it this far." Everyone except Alec, Jace and Simon started laughing, the boys just sighed.

"First of all Jace, I need to know what you have about Valentine and Jonathan. Second, then I'll give you a plan."

Jace nodded. "All we really have is that they still lead the group called the Circle."

Jocelyn gasped, "He still has that running? But, Valentine can't be running it, he trusts no one."

Jace nodded again. "You're right. Jonathan has been running the Circle, but Valentine keeps a close eye on it himself." Clary was deep in thought, when something dawned on her.

"Wait, The Circle, when my father was running it was all about changing the Clave, and he didn't succeed. So, what is Jonathan trying to accomplish?"

Jace shrug his shoulders. "We have no idea. He's been keeping the Circle in the shadows and working there, we haven't seen much of him doing any activity with the group, yet. But, we all feel that he has been "building" up reputation, recruits, the list goes on. Literally, he's trying to get his name out there, and to reclaim its status."

Luke shook his head. "I don't like this. Valentine let his son take over? Valentine must not be able to run it himself, either mentally or physically." Jocelyn nodded in agreement.

They all agreed on that Valentine cannot run the Circle, and Jonathan has taken over for him. "So, Clary, what did your father exactly do?" Simon asked.

"We can handled that question," Maryse spoke up. Everyone looked at Maryse who had her eyes on Jocelyn, Luke and Hodge. They all nodded to let her know she can speak of, the past.

"When the Circle was in formation, he recruited us. Luke, Hodge, Jocelyn, the Herondales, me and your father, Izzy and Alec. All we did, was recruit and train shadowhunters to fit Valentine's guidelines. He thought that the Clave should be removed and a new order placed, although he may be right, he did not choose that right way to execute his plan. When we had gotten enough to maybe take down the Clave, we were defeated and he ran, left us all, except Jocelyn and Luke, they ran with him. But, we forgive each other. He has been in hiding for years since, until he found Jocelyn again."

"I only left him, because I didn't want Clary in his world, in this one. But, Valentine found us and took her. I told her that I left him because I didn't love him when really he took her from me. He came to me and told me if I didn't give her up he would kill me and Jonathan. I wasn't worried about me, nor Jonathan. But, of course, he knew me, he knew how to get in my head. He threaten Luke, and all of us. He would kill us slowly, and we 'would never know'. That I wouldn't stand so I let him take her, and Clary I'm sorry, I really am." Clary looked horrified at her mother.

"Mom…no, I can't get mad, nor can say I'm upset on what you did. I'm just surprised and confused. In a way, I don't mind but in a way I can't stand that. All I know is that my mother gave me up so I could live, and so could of you. He brought me to this world, but treated me as if I was a slave, not a daughter, he treated Jonathan like a soldier. He never made me do anything, just be there. He made Jonathan do everything, until he left.

"He told me he left because he couldn't take Valentine, but I wonder if he was kicked out. Once, he left I was left doing everything. Like, getting supplies, training, and making trades. I couldn't take all the pressure anymore so I left. Valentine never looked for me, because he went back to Jonathan, and now he's giving the orders."

Alec nodded, "well, this explain a lot." Everyone stood there silent. No one knew what to say, everything was already said.

"Well, I guess the plan now, is to prepare ourselves. Gather supplies and keep training. We are not even where we need to be to defeat Valentine or Jonathan." They all agreed. Everyone disbanded and continued talking, especially the elders, of course catching up. Jace thought something was off with Clary, he went to ask.

"Clary!" She turned. "Can I talk to you, somewhere private?" Clary nodded her head, took Jace's hand and lead him to the greenhouse.

"Clary…I don't believe you."

Clary squinted her face. "What do you mean?" Jace looked at her with annoyance.

"I mean, I don't believe your story. Your mother's seems believable but yours? Living with Valentine and you didn't do anything except be a housewife? Yeah, right. You did things with Jonathan. You did jobs for Valentine. I don't believe you."

Clary smirked. "You're good, Jace, almost too good. We'll see how far you'll get, and if anyone will believe you."

She walked away leaving a rhythm of steps on the concrete. Jace couldn't believe it, the girl he started to feel sorry for, was always playing a game. "She's trained to be a spy, and she's doing it good. You better run, little spy. I can't believe I almost fell for you."

_**OOOOH! Where will I take this? Clary is now a bad girl ;) she's the spy. Oooh! Plot twist! Well I hope you guys liked it. What will happen if everyone find out? And, does Jace feel something? Who knows! See ya later ;) -Jess**_


	6. Chapter 6: Let's Talk

Jace watched Clary walk out of the greenhouse. He knew she was trouble, but he couldn't help it. There was something about her. The way she moved or how she held herself high; she wasn't afraid. But, Jace knew he couldn't deny what he felt. It was like a spark lit up inside him. He had to leave when he was young.

'_I can still remember that day, the day I left him. I left Valentine. I did jobs with Jonathan and Valentine, and I never saw Clary. I didn't even know she was there, but her story doesn't fit. She can't sit still when she sets her mind. Clary is…she's something.'_ Jace just paced around the room. He didn't know what to think. He liked Clary, a lot, but he couldn't trust her. He's in too deep, in all of this. Between her and her father and his past.

'_I was brought up by Valentine. I worked with him, and when I couldn't take it anymore and he threw me out I found Maryse. She took me in, and I've been in good business. Then I found out we were rogues, and then I found out about the Institute. It changed me, all of us. And, I'm thankful,' Jace thought._

He walked down and found everyone packing and gathering as much material as the Institute had, and could hold. He saw Clary, she smirked at him. He walked over to Alec. "What's wrong?" he asked.

"Clary." Alec looked at him, questionly.

"What about her?" Jace shook his head, "she's not…exactly what you think."

Alec squinted his eyes. "I mean, she's not…she's a special spy. Not just for us." Alec looked shocked.

"You mean…?" Jace nodded. Clary looked over, as almost she heard them, loud and clear. They went back to work. Clary dismissed her feeling.

'_Damn. Jace is too good, for himself. He may know something. And, I can't hold on, that much longer. Stupid Jonathan, getting himself into messes, he shouldn't. I never asked for this, telling lies, trying to protect my family. Mom, Luke and him. He's not worth my time. But, he's like a fire, burning a hole in me.'_

Clary knew that no one understood. And, that everyone thought she was a traitor. But, she was trying to protect someone, right?

Maryse and Jocelyn had started making dinner, as everyone else gathered and started to chat and reconnect. Clary had walked toward the door, when someone grabbed her wrist and forcefully turned her around. "Where are you going?" Clary couldn't believe who she saw. It was certain blue eyed man.

"Alec! What?!" Alec could hear her nervousness in her voice. She wasn't a good liar.

"Where. Are. You. Going?" Alec looked at Clary as if she was pest.

"Fine, since I can't win. Out. To fix what I started." Alec shook his head with his arms crossed.

"Do what you want. But, stay away from Jace." Clary smirked and started walking out the door.

She was on the sidewalk away from the door, and Alec was closing it when, "Oh, Alec? Do send Jace a kiss for me." And she was gone.

Clary ran down the street to meet Valentine. She walked into an abandon factory. "Valentine!" she screamed. Valentine laughed, and walked down a staircase off in the distance. Clary didn't like the drab, mud and dust all over the place. Garbage and rats here and there. And, nothing but rusted metal, with some new plumbing. Plus, everything's black, as coal.

"Well, my little fiery rogue is back. Jonathan? Come out." Jonathan came out with chains wrapped around his body. He could barely move, and with a good piece of tape over his mouth, he couldn't speak.

"I got them to start your plan. Let some chains off, or let me talk to him. Please." Valentine shook his head, and walked over to a couch. He waved his hand and Jonathan was taken away.

"See, I can't do that. They're not here, and I don't trust you or your brother, daughter. Nice story, by the way. Saying, you were housewife. You wish you were."

Clary understood quite well. Her "lie" wasn't as white, as some may think. She did live with Valentine, but she wasn't a housewife. She was a sort of everything. She would hull the loads, deal with the money, recruit spies. She did everything, even a housewife. But, she never did anything like Jonathan or Jace did. "Yes, you remember quite well."

Clary heard a bang at the door. More, and more. Someone was trying to come in. "Grab my son, and hide him. Well? Go!" Two bodyguards grabbed Jonathan and took off. Jonathan sprang and had out a knife. He grabbed Clary and put it to her throat, when the door swung open.

It had to be at least almost eight o'clock before Jace could tell Clary was gone. "Alec? Izzy! Izzy, where's Clary?"

Izzy was almost drunk, "slightly off", as some put it.

"I d-don't…kno-know," she said with hiccups. "I saw-her..leave..earlier..be-fore we…ate." Jace was sober enough to understand. She left. He wasn't going to let her go.

'_She's too innocent.'_ He found Alec and made him tell Jace where she went.

"I don't know!" Jace dismissed him in disgust.

"Jace! She never cared about you. If she did, it was all a lie." Jace waved him away. He ran, and ran until he found a bodyguard that seemed familiar from when he worked with Valentine and followed him. He barged in.

"Jace! Welcome, son," Valentine said as he released Clary. Clary ran under his arm and into the corner. She couldn't believe he was here. She wiped her neck, and saw red on her hands. She had a slight slit from Valentine.

"Clary," Jace whispered. She shook her head, and walked over to grab the bodyguards and Jonathan.

"Sit down, let's talk," Valentine said as all four of them sat down. At least Jonathan wasn't tied up.


	7. Chapter 7: The Little Spy

"Look, my son, my daughter, my _other_ son. We're all here. How wonderful!"

Jonathan hissed in disgust. "'My _other s_on', I appreciate the love, f_ather._"

Valentine smirked. "Now, let's set the record straight, shall we?" Clary sighed. She knew exactly what this meant.

"So, let's see. Jonathan and _Jonathan_ both worked for me since they were young, but you, Jace, by accident. I remember you were a little boy with no family, and I took you in. Now, Clary you left around the time Jace came in. See, Jace, your family was getting in the way of my "dealing", so I took them out. You were helpless, and me being merciful, I took you in and raised you, and you learned well.

"But you, _Jonathan_, were too rough, impressive, but obvious. Now, _Clarissa_, how do you fit? Well, you did almost everything for me, since _your mother _left. I was hurt, but she didn't care, we were so close to bringing down the Clave. So close, but no she didn't care. So, you filled her spot. While they went and did the outside job, you got stuck inside. _My little spy._ Thanks, for the letters, they helped." She touched her throat, she noticed it was getting worse.

"Clary, what letters?" Jace asked.

"I've been…sending letter…regarding our plan, to bring him down."

Jonathan got up from the seat, and sat next to Valentine. "They were very helpful, little sister."

"No…you LIAR!" Clary got up and almost hit him, when the same bodyguards holding Jonathan held her.

"What is she talking about?" Jace asked.

"I spent months trying to get information on how the Clave planned to take down _my father._ She did it so well, I figure I play along, until I'm not needed and wait. Say, I got captured. She never knew. I worked for him."

"How could you?! I spent hours trying to save you by getting that information, and you were undercover. You…monster!"

Clary stopped fighting the man and sunk into his arms. Jace was in shock, his face froze and he would not say anything,

'_She was trying to do the right thing…we both survived…we both left,' Jace_ thought.

"But, please Clarissa, won't you join me?" Valentine asked.

"_**Never,"**_she hissed.

Valentine waved his hands and both she and Jace were sent down to the cellar.

"Jace, I'm sorry." He looked up from his shaking hands. She sat across from him, in the same cell.

"For what?"

She was almost in tears. "For everything. I pulled you into this. I lied to you, and pretended to be someone I'm not. I just…"

Jace took her hand. "Clary, in the time I've known you, you're different. You put up a fight, you do what you think is right. So, what, as long as you're willing to fix and end what you started, I'll be there. But, you need to set _everyone _straight." She nodded.

Clary noticed the door was ajar, and that there was crowbar not far from them. She started pushing her arm through the bars to try and grab the crowbar. "What are you doing?"

"You'll see," Clary said with sly smile. Jace smirked.

'_I have to get him out of this. He can't be back in this…come on, just a little closer!'_ Clary thought. Clary grabbed he crowbar, and pulled in through. She jammed it into the bars, and pushed and pushed to break the rusted ones. She was able to get almost all the bars broken almost to the top, enough to slip through.

"Okay, there's a back entrance, we go out there," she whispered. Jace nodded.

Clary couldn't help but look, stare, into his eyes. The way they would shine even if there was no light. How, golden and bright they were.

She knew she had to finish this. But, she wasn't ready to do it with him. Clary took Jace to the back entrance. "Go! I'll be right there!" Jace went out and Clary shut and locked the door. "Clary!"

Clary did it for herself, for him. "Jace, I'm sorry, I have to finish this…I don't want you to get hurt…" and she ran off.

'_Stupid Clary…I don't want you to get hurt. I'm sorry, I was so cold.'_ He ran off to get Alec and Izzy.

"Valentine!" Clary screamed.

Jace ran down the road again and took the long way back. He needed to think. '_Stupid Clary, can't she see? Alec was wrong, it was never a lie. Her acting was,' _He thought.

When he finally arrived, most people were asleep or past out, from the party. He found Alec, sober. "Alec!" Alec looked at him with anger. "Clary! She's going after Valentine. Now!"

Alec shook his head. "So? She hurt you, me. She didn't care about any of us, can't you see that?" Jace's eyes began to water.

"No, can't you? She thought she was doing the right thing, she thought Jonathan was captured. Remember how she changed because Jonathan left? It was because Jonathan did…for Valentine. Clary got some information to save him, in reality Jonathan was always trying to get it. Clary can be trusted, not him."

Alec didn't know what to think. He had to trust Jace, since they were _parabatai._ "Fine. But, she has to explain this, to all of us. I can't trust her, but I can you. Get Izzy, we do this alone."

"In the end, it didn't matter huh? He would've gotten it anyway. I just made things easier."

Valentine smirked. He wasn't surprised that she was able to escape, but that she didn't bring Jace.

"So, you left your boyfriend?" Jonathan said.

"He's not…" Clary looked down, at her hands. How he held hers, how she felt, how he did. It all clicked.

"Really? 'Cause he seems to think so…" Clary nodded. They can't know, _never. _

"Well, then join me sister, we call rule this world. Make things anew. Please. For father," he said with a concerning tone.

She shook her head and pushed him away. "I left so I could get away, and not to join again."

Jonathan spat on her face. "Fine, I asked. You said no," he grabbed a knife.

Valentine put his hand on his son's shoulder, "Jonathan, no. She must live. We have other plans that she can be used in."

Jonathan understood, and left Clary alone, confused and irritated.

"Izzy come on!" She struggled against him. "Why? Leave me alone!"

Jace picked her up and dragged her to Alec. "Deal with your sister."

She snapped. "I'm yours too!" Jace smiled.

"Come on, Iz."

They got their gear, and headed toward the factory. "There," Jace pointed out.

They stealthy walked down to the factory and woke Izzy up. "Izzy, wake up," Alec said.

"Huh? Where are we?" She said as she grabbed her head, because of her pounding headache.

"We're going to rescue Clary," Alec said, trying to wake his sister.

"Look, over there!" Jace pointed out to Clary being pushed to a ledge.

"Well, since you won't help us, you wouldn't mind if I get rid of you?" Valentine said, as he grabbed Clary's arm and dragged her out to the ledge and started to push her farther and farther with a gun.

"I've delt with you, for too long. Good bye, Clarissa."

"No, please. Valentine please!"

"Father, please. We can use her." Jonathan grabbed his father's hand.

"NO! I've wasted so much on her! Her and Jocelyn. I shouldn't be mad at you and yet, _I AM_."

Valentine knocked back his son, and punched him out cold. He continued to push Clary to the edge. "You, should've left with your mother."

"No, I shouldn't have." Clary kicked the gun out of his hand. "No, I'm glad I stayed. It made me realize you don't know a thing, about _me." _She had the gun pointed at him. "I learned quite well, who you are, and who you'll always be. I learned that my mother was right, and that my dad was Luke, you were _never _there. Now, this isn't some daughter-father thing, no, this is about your ideas and how I'm in the way. You won't ever see me again. Valentine. _Ever." _

Clary fired once and ran. The bullet hit Valentine right in the shoulder. "_Run away, my little spy. Run away."_

Jace heard the gun. He thought the worst until he her scream and be dragged out by the guards. "Come on!" They all ran, even Izzy. The gun firing had woken her up, good.

"Clary!" Clary turned her head to see Jace running and Alec helping Izzy not far behind him.

"Jace…" Clary's throat had stopped bleeding, but her other wounds from trying to fight the guards that picked her up and was taking her somewhere, somewhere she didn't know, we're now bleeding.

Jace had kicked the man holding her, and he let her go. She scrambled to her feet and grabbed the knife Jace was holding. She threw the knife and it landed in his back. The other guard had come around the corner and tried to shoot Jace and Clary when the gun went off and they both saw the bullet hit the building.

"Alec…" Clary said. Alec had fired his bow and the arrow landed right in the man's chest.

"Come on, I don't want to be here, when the cops come." Clary followed Jace. Alec and Izzy followed them as they made their way back to the Institute.


	8. Chapter 8: A Blade in the heart

A/n: Hey! I'm so sorry I haven't added any chapters but I'm back! School started and I spent most of my time reading _The Infernal Devices, a_nd to be honest, kind of forgot to update, (sorry!). But I'm back with a new chapter! Enjoy!

Izzy finally had woken up and they were all running back to the Institute. No one wanted to talk about what happened, not here, not now.

They ran through streets and alleys and finally made their way back. They could hear the sirens of the police cars coming down the street. Someone was bound to either heard or seen what happened.

When they went inside Clary went to find Hodge. She couldn't find him. She looked in every nook and cranny and could not find Hodge. She finally heard noises coming from the library and found Maryse, Luke and her mother tied up with Hodge sitting in a chair by the statue of _Raziel. _

She saw the look on of all their faces. A look of fear, love, and caution; telling Clary to run away. But, she couldn't; she couldn't leave them. She had to do something.

They were in the middle of the room, right in front of the statue, all bound together by rope. Hodge sat there, in a velvet, gold chair staring out the window. He still had his gray hair, but his eyes seemed more gray than normal, almost ghostly. He wore a suit and tie and kept twirling a stele in his hands.

"Hodge…?" Clary spoke softly. Her family, even Maryse had grown on her, now was in hysterics trying to get her to be quiet.

"Clary," he spoke, getting up out of his chair.

"You know, Clary, you're story is quite interesting, but so is mine." Clary looked at him. She was scared, but she would never show it. She remembered living with her mother and Valentine. Her mother left and gave her the option to stay or to come. She left, but, she came back. She came back because she missed her brother, and the city. Although her mother said he took her from Jocelyn, he needed leverage and he twisted Clary and Jocelyn into letting her go. She knows now, she should've never came back, but that was then. She remembered she did all the inside jobs. The paperwork too, and when Jonathan left she felt lonely and things got worse. Jonathan was there off and on, and that's when Valentine found Jace, that's when Clary left. He used him to fill the hole, but then Jonathan came back, only to leave again. But, by then we all left. Clary had, and Jace had found Maryse. They were so young, no older than twelve. "Hodge, what have you done?" she questioned.

He stiffened. He knew, that this would end, in something awful, but he couldn't take it anymore. "Clary, I've spent years trying to get Valentine to remove the curse the Clave put on me. They would only allow me to teach, I couldn't do anything more, I couldn't even leave this place, without breaking the tracker on me. But, no matter how many times I was able to get you or Jonathan to work for him fully, he would never keep his end of the bargain. So, now I'm collecting."

Clary never knew. He was preparing her to work for Valentine completely. She heard footsteps, Jace, Izzy, and Alec were around the corner. She had to finish this now. "Hodge, please. Don't follow Valentine anymore, I don't want to see you-"

Valentine burst through the window shattering glass everywhere. Jace, and his siblings burst through the door to find Valentine had a knife, again, to Clary's throat, and Hodge crawling to Jocelyn and the rest.

"Valentine!" Jace screamed.

"Jace! Get out of here!" Clary yelled.

Jace had his blade out ready to strike. His face was glowing with sweat. Alec and Izzy stood right behind him in astonishment. No one knew what to do. Hodge had gotten up and grabbed a vase. He swung the vase at Valentine's head and he stumbled away from Clary. Clary ran to her mother and untied the ropes.

"Valentine. You will set me free." Valentine grabbed his sword and charged toward Hodge. Hodge pulled out his and kept blocking as Valentine started to push him farther and farther towards the wall. Clary ran and got Jace and told him to get her mother and the rest. Clary ran to find a sword. In the background you could hear the clink and clash of metal to metal. Hodge had gotten a cut on his face as where Valentine on his leg. Hodge noticed his shoulder was bleeding. It had not healed enough.

Clary ran out of the library heading toward the weapon's room, and was stopped by Jonathan, "_Hello Sister," _he hissed.

"_Jonathan._" Clary stepped back. She hadn't reached the weapon's room, but, she was in the hallway, just close enough. She could hear swords still clinking. She knew she had enough time to wound Jonathan and run.

"What do you think you'll achieve from working with Valentine?" she asked.

Jonathan chuckled, and it left a smirk on his face. He crossed his arms and put his sword in his sheath. He walked closer to Clary and stroked her face. "You're so predictable," he said. Clary flinched and Jonathan backed away. His eyes were still black as coal, and his hair as white as snow. His demeanor was cocky and he knew exactly how to pull strings and tug chords.

"Mostly, recognition. To not feel powerless, to have power. To be known, I could go on." Clary noticed that he was serious. He was walking around in a circle, waving his hands as he talked, as if it was a normal conversation, but Clary knew he was doing something, but what?

Jonathan kept talking about his dreams and wishes. Clary was able to move toward the room, but was startled by his voice. "Oh, Clary I'm not blind. I wouldn't go in there. You wouldn't win anyway." It was like he was answering every question or idea Clary had. The swords stopped. Clary turned at the moment she heard a scream. Just like that Jonathan disappeared into thin air.

"Izzy...Hodge!" Clary knew that was Isabelle screaming and she ran. The only reason why Izzy would scream is not a good reason.

Clary ran in to see Izzy crying and Alec holding up Hodge. Jonathan and Valentine were nowhere to be found and it seemed Maryse as trying to get a hold of Magnus. Jocelyn and Luke were trying to calm down Izzy and Jace stood there frozen in time.

"Jace…" He turned and ran up to her. Her hugged her and didn't let go. She looked at his face, he was so worried. She thought maybe they both were reckless, on occasion. She looked around, as he was still holding her. "Jace…can you do me a favor and let go?" He let go and smiled.

"Now, do me another?" She kissed him. She reached up and pulled him down to her. She ran her fingers through his hair. She let it all go, everything she was hiding, everything she was scared, she let go. He responded by holding her tightly, pulling her into him. Clary loved how he held her, and the way he smelled so sweet.

"Thank you. I'm sorry," she said. He smiled.

"Anytime, but you know they're all wondering what's going on?" She nodded and walked toward Hodge.

"Maryse is getting Magnus and a Brother. You'll be fine, Hodge."

Luke, Alec and Jace got Hodge up and walked him to the Infirmary. They would have to wait.


	9. Chapter 9: A New Story

Brother Enoch had finally come, and had made preparations on Hodge and began his healing. He told that no one could enter his room, so everyone waited in the library. The library was now filled with broken glass and ripped furniture and cloth. A draft was coming through the windows, since they were shattered. Blood drops stained everything. The library was not clean anymore.

Maryse was talking to Magnus to see if anything could be done, to stop or figure out Valentine's plans. But, according to Magnus, no one knew where to start.

It dawned on Clary that her mother and Luke hadn't be introduced correctly. She gathered her friends and brought them over to her mother and step-father.

"Jace, Izzy and Alec, this is my mother Jocelyn, and her fiancé Luke Garroway. They raised me, after I left Valentine," Clary sat everyone down, including Maryse and Magnus. She decided that now everyone was going to come clean.

"I think we should set everything straight," she said as she looked up at everyone. She took a deep breath and let it out. She thought every moment this night, every moment with Valentine or Jonathan. It hurt to open wounds, but it had to be done.

"My name is Clarissa Morgenstern, and my father was Valentine, my brother Jonathan, and my mother Jocelyn. My mother asked me when I was six if I wanted to go with her when she left Valentine, and I said yes. When I was nearly seven I realized I missed Valentine and Jonathan and went back to live with him. He tricked my mother and I into letting me go, by me missing him and blackmailing my mother. He trained me every day, and eventually I started doing jobs, and paperwork for him, off and on. I had wanted to come back after I realized how cruel he was, but my mother couldn't let me, it was too risky for both of us. Out of desperation, I ran and left, when I was old enough. But, before then Jonathan came and went and Jace came around when I was eight, and he started doing jobs, filling Jonathan's place. Jonathan came back and all Valentine worked with either Jonathan or Jace on one mission, never both. Jonathan left for the last time and it was just Jace, but I never knew he was there when I was there because right around when he started working for Valentine I left. I left when I was nine and I assume Jace did the same. I have lived with my mother since then. Jonathan had his own place, I had no idea what he was doing. This year Jace and his siblings came and soon after Jonathan left. Thinking he needed help and I gave Valentine information. Now, I know Jonathan was always working for Valentine and that he is not my father, and never really was. And, I'm sorry Jace that he raised you, until you left and found the Lightwoods."

Clary had said that out loud and then left to her room. Jace sat there thinking he should do the same. He sat upright and brought his hands to his lap and clasped them.

"My name is Jace Lightwood. Valentine took me in when I was very young. I started doing jobs when I was nine. When I was twelve he gave me up. He didn't like the way I did my jobs and took me to an orphanage for spies. I found the Lightwoods through the agency, I was told I was Jace Wayland, and that Valentine and the Lightwoods were helping a family friend's son. I had gotten the Lightwoods into some trouble here and there, so we went into slight hiding. When were ready to reclaim our status, "by coincidence" Valentine went back to his horrible habits, reclaiming his status." Jace choked up. That was all he could say, because that was all that really stood out.

"Thank you, Jace and if you see Clary tell her thank you, as well," Magnus said, shedding a soft smile for the boy.

"Well Maryse, I have to go report this to the Clave," Magnus said and with a turn he was gone. Magnus had introduced himself, although everyone knew him, and what he was. He would be a great help, when called upon.

Everyone was quiet, until there was knock at the door of the Institute. Maryse went to answer it, when she returned, there was a skinny brown haired man.

"Simon?" Jace said. Everyone was in shock. What was he doing here? He was holding something, a letter? He seemed tense and worried.

"Where's Clary?" he asked. Simon seemed distraught. He was very frantic and couldn't sit still.

"Simon, what do you have?" Simon looked down at his hands and handed the letter to Jace. Simon's brown eyes drooped downward, as he kept pacing.

"Maryse this is a letter from Valentine…?" Maryse came running over. Her ink black hair swinging. She grabbed the letter and started reading.

"'Clary_ is of utter importance to me…she will not escape me, again. I will be back'," she said as she_ sat down. "He's coming back, he won't stop until he has her. But, why did he send this to you, Simon?" He shook his head. It was a very intriguing question, but Valentine had a point to sending it to Simon.

"Wait, Simon knew nothing of this that was going on. Valentine sent it to scare Simon, I guess," Izzy said. She had close to figuring out why Valentine sent the letter to Simon, but he was clever, he wouldn't just give it away.

"Look, everyone calm down. It's late, we can figure this out in the morning, when Hodge is well again. Brother Enoch will be a while, I think we should do what Clary did, and go to bed. Simon if you want you can stay here for the night," Maryse said as she gathered her things and left.

"I guess I will," Simon said.

"Here come with me." Izzy got up and showed Simon where he could sleep and where the bathroom was.

"This is Clary's room, and that's mine. Yours is around the corner." She walked around a corner and showed him the door. She let him in and get settled.

Simon couldn't believe it, he was back in this mess and he didn't know where he belonged. He laid there for hours before falling asleep. All he could think about was Isabelle. Her ink, black hair. Her dark eyes, and the way she walked. She had a lot of confidence and wasn't afraid to show it.

He was finally able to rest his head and fall asleep. For once he slept peacefully in a place he didn't know. He figured he would have to become friends, but Clary still had him worried.

**A/n: Heads up! Yes, there will be Sizzy, yes there will be Malec. But, I have to work my way there. And, a shout out to all of you who favorite or follow my story you have no idea how much it means to me :'). Anyway, so I hope you liked this chapter! And, we'll see where it goes!**


	10. Chapter 10: Another Day

The next morning Maryse got up and headed to the kitchen to make breakfast. Magnus stayed the night as well, he slept in the same hallway as Alec, Simon and the rest. Magnus went down to check on Hodge, when he bumped into Alec.

"Oh…excuse me, Magnus," Alec said. Alec was shy and he kept his head down, holding a muffin. Magnus looked at him and smiled. Alec was like a little bird who was scared to fly.

"No, excuse me," Magnus said placing his hand on his shoulders and letting himself around the boy. Magnus continued his walk to the infirmary. Alec stood there watching him leave, then turning to go to his room.

Clary was the next one to get up. She put on her slippers and headed up to the greenhouse. She found a bench, near the edge of the top. She sat down and watch the cars go by, on the street down below. She heard the leaves crinkle, she looked behind to see Jace holding a cup of coffee, toward her. She took the cup and turned her head back toward the city. Jace sat down next to her. He sipped on his coffee as Clary held hers in her hands, staring down in the cup, watching the steam come up the cup and blow away.

"Jace, do you actually love me?" she said. Ever since they kissed it's been on her mind. She knew there was something there, but every time she thought, it somehow was shot down. She didn't know what to expect, she didn't know what to think. It was a splurge of the moment. Jace smiled, he sipped his coffee and pushed his hair back. Clary noticed his smile, and the little chip in his tooth.

"I'm going to be honest Clary, I think I do," he said as he turned his head toward her and smiled. She turned her head, and her eyes widen with joy. She was so happy, but she didn't know how to react.

She sat there just staring at him. Watching him glow against the rising sun. "Yeah, I think I do too" she said, as she brought the cup to her lips and sipped the coffee away.

…

Jace said he had to go, then he went off to the weapons room. Clary got up and headed to the kitchen. She got there, washed her cup and sat on the ledge of the bay window in kitchen. She thought of what would happen next. Maryse had already made breakfast and headed out. She was having a meeting with some of the Silent Brothers.

Izzy came into the kitchen, "hey Clary!" she said as she walked over and made herself some coffee. Clary looked over at Izzy, but then returned to the window as rain started to fall. Izzy grabbed a plate and sat with Clary. She sat her cup on the table and shoved a bite into her mouth. "What's wrong Clary?" Izzy asked.

She sighed then began, "all of this," she continued, "everything, Iz. I've been tricked, and lied too. Everything I know is now the truth, and I'm happy, but at the same time, I don't know what's going to happen and I'm scared, I guess," she said laughing at the end.

Izzy laughed. She set her food down and swallowed before she could choke. "Clary, you are one of the strongest people I know. You don't take no for an answer. It'll be fine. You got all of us, we won't ever leave. I promise," she said winking; "and, I think Jace has this thing for you," she said sarcastically. Clary punched Isabelle lightly and continued to chat with Izzy.

…

Maryse met with Brother Enoch in the Silent City. The Silent City was the name that was chosen by the Clave, for its secrecy. The city is a place for the brothers to gather and live, and to watch over the wounded and fallen spies. The Brothers are a special group of men who have been special volunteered to be trained in medicine to heal the spies of the Institutes. Maryse approached Brother Enoch. She stood tall and strong, like she wasn't afraid of anyone anytime.

'_I assume you have come here on behalf of the wounded one?' _She heard in her head.

"Yes, I wanted to know how he was doing, since you brought him here with you, while Magnus and I interrogated Clary and Jace," she responded.

Brother Enoch waved his hand forward for Maryse to follow him. She followed Brother Enoch down to the cells to find Hodge laying on one of beds in a cell, with the cell door open.

'_He is not well. Valentine has placed a powerful poison. We have extracted the poison from his body, but the effects are killing him.'_

Maryse was saddened. She knew everyone at the Institute would be very emotional. Some might cry, some might be angry, but she knew the outcome. He was already so weak, it would be hard to carry on.

She said her goodbyes to the Brothers and headed back to the Institute.

…

Meanwhile at the Institute everyone was training. Clary was trying to show Jace how a stele worked. "Jace, it's a sword …Jace! No!" she said as Jace threw the knife and hit the dummy but tearing Alec's jacket at the same time. "Well, at least you hit the bullseye," Clary said. He accidentally grabbed a knife instead of the stele.

Alec was still in shock. "AT LEAST?! He could've made a gash in my back!" Jace laughed went over hugged his parabatai. Clary brought Jace over and let Alec finish his target practice with his bow. She sat him down and laughed.

"You definitely need more practice. Now, as I was saying earlier. A stele is a long, slender wand-like piece of metal, obviously, but what it does it what you need to know. Each stele can be custom made to each person, but serve the same purpose. It injects an ink-like stream of vitamins and things to boost out abilities for a time, like a tattoo needle, into the person's skin. It comes in handy," she said.

"Why do I need to learn all of this?!" Jace said whining.

"Because, things have changed since you last worked with Shadowhunters," Isabelle said politely with a hint of annoyance.

Jace poked out his tongue, which made Clary, Isabelle and even Alec laugh.

"Aww, did we hurt little Jace's feelings," said Alec. Jace punched Alec and Alec blushed at his own shock. Jace laughed.

Maryse walked in, shutting them all up. "I need to see you four, now."

Isabelle looked at Alec. "Mom's not happy," she said.


	11. Chapter 11: Reappearance

Maryse gathered the four children and brought them into the library. The room looked a little better. The glass had been swept up, and the ruined things removed, but nothing was replaced yet.

She sat them down on the couches and she grabbed a chair out from the corner and sat in a circle with the gang. She sighed and finally spoke, "Hodge isn't doing well." They all looked intently to Maryse for better news and that maybe there was something they could do. "The poison is out of his body, but according to Brother Enoch, the effects are killing him."

Maryse waited for a response. Isabelle and Alec kept their hands locked together and their heads down. Jace stared off into space, and looked lost in thought. Clary looked around at the others. Jace turned his attention toward Maryse and locked his hands together. "Can we see him?" he asked. Maryse nodded.

"But, the Silent Brothers, are _silent," _she finished under her breath. She turned and looked at Clary. "I assume you never met them?" Clary nodded.

"Correct. I've never actually met them, I just know they exist," she said. Maryse nodded and wondered what to say next. She figured she should explain them more in detail.

"Alright. The Silent Brothers go through rigorous training in medicine and surgery to "work" in that department. They know a lot of ins and outs of the Shadowhunters, so they are permanently kept quiet. The have a device where you will hear them in your head, but their lips will not move, so don't freak out."

Clary seemed quite intrigued how that was possible. "But, how is that possible?" she asked.

"Some say that their lips are sewn shut, and that the Clave made a device to where they could always be one step ahead of enemies because they can read minds. How or why…we don't know. Some say, when kids are born they're given receivers, as in they shoot one in your arm or whatever," Jace said. Clary's face became so red and so shocked. He started laughing and apologizing, saying he doesn't know if it's true or not. Everyone started to chuckle at Clary's embarrassment.

Clary realized that they knew Hodge better than she did and that she knew so little of the world she put herself in. She realized no one knew more about the shadowhunters she grew up with here, than them, since they grew up with them first.

…

They were gathering things so they all could go down to the Silent City and say their goodbyes, when there was a knock on the door. Clary dismissed herself and went to the door. She opened the door to find a women with red hair staring back at her.

"Mom!" she exclaimed. Clary brought her mother to her room where she was gather her final touches to put together.

"Mom, what are you doing here?" she asked. Jocelyn was beautiful. She had red, flowing, curly lock like her daughter and those lovely green eyes. Jocelyn thought long and hard on how to explain her sudden reappearance, since the last time she was here she wasn't here for very long.

"Well, the simplest way to put it is, that it seemed safe," she said. Clary looked at her mother with confusion. Jocelyn chuckled to herself looking at her daughter's confused expression. "I heard that Valentine had been weakened. I thought maybe now would be a good time to remerge fully with the world I once lived in. And, Clary I know you're one who brought down his strength." Clary nodded. Jocelyn smiled and held onto her shoulder as they walked down the halls, and on occasion having her scarf go into Clary's face.

…

When they reached the library where everyone was to meet Jocelyn and Maryse smiled at each other and hugged to go sit down and catch up. They all sat down and chatted to past the time when Clary's phone buzzed. She looked at her phone and noticed it was from Simon. She set it aside and returned to chatting. Her mother noticed and got up to check Clary's phone.

"Ah, it's from Simon. I saw him earlier, he's probably telling you I'm back home," said Jocelyn. Clary looked at her phone and wouldn't you know, she was right. Simon talked about how excited he was to have her back in town and have things seem normal again.

"Only if he knew the truth," Clary said.

Jocelyn had a puzzled look on her face. She sat down next to her child and Maryse dismissed her children, even Jace, away to finish gathering things, finally. Clary looked at her mother with careful eyes. Jocelyn could tell she was scared. Clary held her hands together in her lap, as Jocelyn put her arms around her daughter.

"Look, I know this may seem rough or hard, but always know you have me. I'm not afraid anymore and I'm staying. You have friends that will never leave you. Clary, it's okay, I won't let him or your brother near you, I promise," Jocelyn said.

Clary nodded her head and said, "Thanks mom."

…

They finally arrived at the Silent City. Jocelyn, and Maryse stayed behind and watched as the group made their way to say goodbye to Hodge. Alec spoke for him and Isabelle. Jace spoke for himself and Clary spoke for her and her mother. Each said something that reflected what happened in their lives, and how he was there.

"We grew up with you, Hodge. You taught us so much, and I know we'll use it to good use," Alec said.

Jace walked up to Hodge next. "I'm not saying goodbye, just know that you taught me to venture out, and for that, I'm grateful," he said.

Clary walked up last and spoke softly. "Hodge, I don't know you, like the others do, but you do mean something to me, thanking you for teaching me, when I didn't know anything," she said.

Clary started to walk away when he whispered something. He kept whispering it, but could hardly breathe. Clary noticed and walked back to him.

"Clary, I'm sorry," he said. Clary shook her head, asking what he was sorry for. "Clary, just know, I'm sorry," he said again. Clary was slightly freaked out, but dismissed thinking ill of a dying man.

…

On the way back Clary checked her phone again and he said he was still having a party with all his friends and family just so they could all be there for Rebecca. She asked who wanted to go and everyone said yes. So, they all headed over to Simon's house.

When they all arrived everyone went to certain areas. Clary said hi to Simon, then went to talk to Luke and Jocelyn joined him. Jace followed Clary and chatted with her. Maryse talked to Magnus about Hodge and what exactly happened, everything is still fuzzy, is what she determined. Alec followed his mother as Izzy went after Simon.

"Simon! Hey! So, I see you made it back home," she said. He nodded and explained how Magnus took the letter and was going to see where it came from.

"So, I've been trying to get comfortable at home again, I guess," he said to finish his thought. He excused himself as he went to go get something to drink. Izzy made her way to Clary and Jace to chat.

Clary noticed how Izzy was talking to Simon, and asked her "so…are you interested in him?" Izzy blushed but threw off her blush by saying she wasn't, just wanted to get to know him. They kept talking and Jace noticed something.

"Izzy didn't you say he was getting a drink?" She nodded and asked why. "Because, he's been gone for over ten minutes."

Clary started spewing reasonable answer as to why he hadn't returned that's when Jace moved toward the kitchen.

"Really? Then what is this on the floor?" as he pointed to red droplets on the floor, very thick; it looked a lot like blood as Jace had thought.

They followed the trail to find the basement door opened and went down the steps. They walked around calling out for him, "Simon! Simon? Simon….?"

Who they find scared them all. "Hello, sister," Jonathan said.


	12. Chapter 12: Disappearance

_**A/n: SOOO, PLEASE FORGIVE ME. I know I haven't updated in like four-five months. I had writer's block and then I decided I wanted to edit so I finally finished editing this story so, I WOULD ADVISE GOING TO GO REREAD THE OTHER CHAPTERS, PLEASE and school and just stuff in general didn't help. SO, THANK YOU ALL OF YOU WHO FOLLOW AND FAVORITE, IT MEANS A LOT 3. So, review please and enjoy! And, just a note. I know sometimes the characters are little out of how Cassie wrote them, so forgive me for that.**_

…

They all stood there in shock. Baffled at how he got in and why he was here. Izzy noticed that Simon was tied up in a chair with a giant gash on his forehead.

"_Sister_, you shall get more information in the future," Jonathan said as a cloud of smoke came and clouded the basement reducing visibility to zero.

"Just like that he's gone," Jace said after the smoke had clear to find Simon and Jonathan had disappeared.

Izzy had started to break out into worrying about everything. "How are we going to tell his mother? What if he dies, or something?!...," she kept repeating the same things and Jace had tried to quiet her down.

Clary still stood there in complete shock. She had her best friend taken away from her and her own brother was the one who took him away. She felt as if she was falling apart but she knew that she couldn't give in to her emotions.

Clary ran up the stairs leaving Jace and Izzy behind. "Clary, where are you going?!" Jace said as she busted the basement door open and entered the party.

…

It was now late at night and most of Simon's family had left and who was left was all the shadowhunters, Simon's mom and Rebecca.

"So, he's just gone…for now?" Rebecca said. They all sat in a circle around her trying to get her to understand where she now stood in the middle of everything. Jace had said one word about Simon being gone and she had enough. She didn't want anything to do with them or him. "He's not my son," was all she said.

Rebecca now worried about him and her mother. "My mom, she feels like he left her and not that he was kidnapped. Is there anything I can do to get him back?" Clary could hear the desperation in her voice.

Clary could understand Rebecca wanting to help, but she couldn't understand why Simon's mom didn't want her son anymore. Clary hoped that maybe it would change by the time they would get Simon back.

Alec had suggested that maybe they all should leave and head back to the Institute and take a load off. Tomorrow would be a better day to start to fix this mess.

…

Izzy was sitting in the chairs by the kitchen table looking out the window. There was only one person on her mind when Clary walked in and stood back in shock to see Izzy up early and in the kitchen.

"Izzy, is something wrong?" she asked. Isabelle shook her head and continued to look out the window. She rested her chin on her hand while Clary fixed herself some cereal.

"C'mon, Izzy. I know something's wrong…why don't you tell me?" she cooed as Clary sat herself down across from Isabelle.

Clary crunched her cereal staring at Isabelle, waiting for an answer. Izzy kept looking out the window, and wouldn't give Clary a hint at all. Clary cleaned her bowl and left Isabelle alone in the kitchen as she went to find Jace.

Clary found Jace in the training room preparing to practice. "Jace, can I ask you a question?" Clary asked startling Jace. Jace didn't expect to hear someone walk in and start asking him questions. He stopped in his place and looked at Clary and replied to her to go ahead.

"Do you think Izzy cares about Simon?" she asked.

Jace thought about it. "Izzy panicked when Simon was hurt and suddenly disappeared. She seems to care about him, so to answer your question, yes."

Clary nodded her head and headed out letting Jace continue his training. Clary went downstairs using the elevator, listening to it scratch and then stop, looking for Isabelle.

She found Izzy in the kitchen. It seemed the kitchen was the place for her and Izzy as was the weapons room for Alec and Jace.

Izzy was sitting alone staring at her phone, for what Clary assumed, waiting for something from Simon.

"Izzy what's wrong?" Clary asked. Clary sat down across from Izzy, staring at her until Izzy looked up to answer. Isabelle had dark circles under eyes as if this situation has been eating her alive.

"Clary, I can't stop thinking about Simon. I don't know what to do. I want to go look for him myself, but I shouldn't. I should've kept track of him," she said with her voice weak.

"Izzy, there was nothing you could do. How would you have known before any of us that Jonathan was going to show up and kidnap him?" Clary said hoping to have comforted her friend. The situation with Simon had actually been eating away at Clary too. She had a nightmare the night before that Simon had been turned into some sort of monster by Jonathan.

"Look, Izzy, I've been worried sick about Simon too. I've had nightmares and I don't know what to do either," Clary said.

Izzy had seemed to have calmed down enough to where she wanted to sleep and would talk later. Clary had let her go and decided she couldn't wait anymore. She was going to go after Simon, alone.


	13. Chapter 13: Searching

Clary felt the need to go find Simon, she had too. She could not let her best friend just sit there, wherever he is, alone. She knew Izzy was scared, Jace felt more sympathy for them, but Clary knew deep down he cared.

She didn't know where he was, or what she needed but she did her best. Clary went to the weapons room to gather a dagger and a seraph blade. She tried to figure out where Jonathan might've taken him; where Valentine might want him.

All she came up with, was somewhere dark and hidden (obviously), but something else caught her attention, and that was how Jonathan was able to disappear out of the room so quickly. There was one person she wanted to see first. Magnus Bane.

She left as soon as she could without drawing attention to her. Clary could handle herself, and she didn't want to cause more trouble than she already is.

'_Simon, please be alright,' w_as all she could think of as she made her break and headed back into enemy territory.

…

She got a cab and headed toward his house. She knew he had to know something about Jonathan or Valentine or where, something that she didn't know to help her, since she had nowhere to start.

Magnus Bane was the most well-known and respected "warlock". Warlock is a term in the world of spies referring to a class specialty, such as weapons, knowledge or in his case, disappearances. His work is so good, some have referred to it as magic.

Clary reached his house, to which she's been many times. His house was a nice-sized apartment fit for a small family, but is now full of his work and his cat, Chairman Meow. His apartment was filled with glitter, and a sense of formality and comfort. It was open, big, but still had a comfy feel to it.

Clary had been here many times. Her mother would bring her here every once in a while to refresh her daughter on how to disappear seamlessly, if she ever needed too. Clary was already afraid that one day, she would have to.

She knocked the door, and the door swung wide with Magnus holding the door wearing an opened purple robe and black shorts, with black slippers.

"Hello, darling. What can I do for you?" he said with a sly smile. Magnus was always happy to see Clary when she would come on her own, since that mean he could actually put his work to use.

"As usual, I need to find someone," Clary spoke softly, entering the big living space.

Magnus went around the corner to find books, upon books, to help specifically find the materials used. Clary thought of how over the years, Magnus has become more flamboyant. He holds many parties to show off his skill in firework displays and things as such.

"Okay, Darling, who we looking for?" he said with focus.

"Valentine."

…

Jace went looking for Izzy, hoping she could help him with a question. He found her in the kitchen looking heartbroken.

"Izzy, what's wrong?" he said. Jace hardly ever see Izzy so sad. Izzy never cries unless she's super frustrated, or truly hurt.

"I don't know," she whispered. "I don't know what to do. Jace, there's nothing for me to do…I just don't want…" she trailed off. Jace went and sat by her. He let her rest her head on his shoulder.

"Iz…" he whispered turning to face her.

"I just don't want Simon…to end up like Max…" she said as tears finally rolled down her face.

"Iz, that won't happen. I promise."

…

Clary looked at Magnus, as he widened his eyes. His eyes were an amber color, and the pupil resembled a cat's. According to him, it was there from birth.

"Clary," he said firmly.

Clary knew he was not happy about what he was doing but in her mind if she could find Valentine, Jonathan would be there too.

"Look, Jonathan took Simon. I figure, if I can find Valentine, Jonathan's there as well. It's worth a shot," she said as she shrugged her shoulders. Magnus gave her a sigh and brought in a computer. He knew she was right, but didn't want to do, mostly for her safety.

Magnus asked her questions about the scene when they vanished. She explained to him about the blood, and what he said, and with a cloud of smoke and a spark of light he disappeared.

"Well, this sounds like, something simple. Probably, a whole in a wall, and a mini explosion to cover the escape. But, I have another idea that might fit them better. A theatrical performance, almost," he said with a smirk.

Magnus flipped through his books and found a special rune for invisibility. "This is a very unique, and new rune. Of course, a stele shoots a chemical that enhances an ability. This rune, like I said makes you invisible, so he could've just slipped away right in front of you, without you knowing. That seems more like him."

Clary knew he was right. "Is there any way to trace it?"

Magnus shook his head. "Not unless we went to the sight, and hope to find a residue." Clary knew that was a long shot. A rune like that is meant to be quick, and to keep it at full strength the stele doesn't leak, or leave a residue, just mark like a scar.

This was going to be a challenge, and Clary was still waiting for something from Jonathan. '_There will be more instructions, _Sister_,' _was all she could think of.

…

Izzy had finally stopped crying and had actually fell asleep when Jace looked at the clock and noticed it was nine at night. He woke her up and helped her to bed.

He headed toward the library located not far from the weapons room. It was grand when he walked in. Jace remembered the way it looked from when he was young. All the books lining the walls and the glass boxes full of unique, precious, weapons. Everything an institute needed to thrive on its own.

Jace lay down on a couch and started to drift off when he heard footsteps and a person sat in the chair beside him.

"I see you put Izzy to bed," the quiet voice said.

"Yeah, she was pretty upset about Simon," he said placing a hand to his forehead.

"I think she cares for him. I don't know why though…"

"Well, don't we all have our preferences?"

"Jace, for once you sounded…not sarcastic," the man had said, giving a playful tone.

"Alec, how dare you think less of me?"

Alec smirked. "Somethings never change," Alec said as he got up, patted Jace on the leg and walked out.

…

"Magnus, it's late. Are we going to do something? I _need _to find Simon," Clary said urgently.

She was started to get antsy. She was itching to just forget and walk out and go back to the Institute and listen to her brother. But, she couldn't.

"Clary, I'm doing the best I can." Magnus had found a tracking device to where if the person is "chipped", the chip can be tracked. But, you have to know the chip's number to track it. That's what took all the time (finding the number). And now, they finally got onto trying to track it.

Some shadowhunters describe the chip as another rune, basically, but it's more of a weapon made by the Iron Sisters.

"Is there any easier way, like the having the sisters help?" Clary asked, as she paces and can't sit.

"No, darling. The Iron sisters are very secretive, they make things like this for only their knowledge." Clary knew he was right, since they were the creators of all their weapons.

They continued their work until it was at least midnight, and this was the longest Magnus would've spent doing his magic. When it was a bust.

"He must've took the chip out," he said when the doorbell rung and I letter was slid under the door.

Clary ran over to the door as Magnus followed. Magnus opened the door to see no one and closed it.

Clary picked up the letter and froze. She hated was written on it; her worst fear at the moment.

It was the "_instructions."_

…

**A/n: HEY GUYS! IM SO SORRY IT TOOK ME FOREVER TO UPDATE! I finally have the time and I've decided that every night I'm going to write and publish when I can so that I don't push stuff off for months. Thank you to all of you who favorite and follow this story, it means so much! I know the ending is cheesy, forgive me. To all who review(ed), thank you it really helps. SO, please review and thank you so much! Love you 3 -Jess**


	14. Chapter 14: Author's Note

**Announcement:**

_So, I won't be updating for a while. I'm so sorry that I've left you hanging for months! The Holidays came around and I didn't have time. Lately, I've been working on one story at a time so that I can put everything I have into that story. At the moment, I'm working on 'You' a romance short story on so when it's finished in a few chapters, i'll be returning to this story. :) I'M NOT ENDING THIS STORY._


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